Contacts of the strand formed by residues 54 - 65 (chain A) in PDB entry 5NXR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.0 36.1 + - + +
51A THR* 3.0 44.4 + - + +
53A GLN* 1.3 77.1 - - - +
55A THR* 1.3 61.0 + - - +
84A LEU* 4.1 25.1 - - + -
85A LYS 3.8 13.2 - - - +
86A PHE* 3.9 23.3 - - + -
312C PHE* 4.2 19.3 - - + -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 5.1 11.3 + - + +
48A THR 3.1 16.2 - - - +
49A GLN* 2.9 35.2 - - + +
50A ILE* 3.8 4.9 - - - -
53A GLN 4.0 2.3 + - - +
54A LEU* 1.3 75.2 - - - +
56A GLY* 1.3 63.9 + - - +
57A PHE* 4.4 1.1 - - - -
84A LEU* 3.4 5.4 - - - +
85A LYS* 2.9 54.6 + - - +
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 3.3 5.2 - - - +
48A THR* 2.7 51.4 + - - +
50A ILE* 3.4 11.2 - - - +
55A THR* 1.3 76.0 - - - +
57A PHE* 1.3 60.3 + - - +
83A GLY 3.4 8.1 - - - -
84A LEU* 4.2 0.4 - - - -
316C MET* 4.0 11.2 - - - -
350C TYR* 4.4 1.1 - - - -
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 3.1 13.0 - - - +
47A ASP* 4.4 13.9 - - - +
55A THR* 4.4 1.1 - - - -
56A GLY* 1.3 76.6 - - - +
58A GLY* 1.3 59.9 + - - +
81A TYR* 3.9 23.8 - + - -
82A ALA* 3.3 4.9 - - - +
83A GLY* 2.9 64.3 + - - -
84A LEU 3.6 15.9 - - - -
85A LYS* 4.0 17.0 - - + -
91A SER* 4.3 11.4 - - - -
92A ILE 3.8 8.5 - - - -
93A ASP* 3.8 18.8 - - + -
316C MET* 4.3 1.1 - - - +
350C TYR* 3.9 10.3 - - - +
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL 4.6 0.2 - - - -
45A LYS* 3.3 4.2 - - - +
46A GLY 2.8 31.3 + - - +
57A PHE* 1.3 79.2 - - - +
59A ARG* 1.3 61.0 + - - +
81A TYR 3.4 10.5 - - - -
82A ALA* 4.2 0.2 - - - -
17C VAL* 4.3 6.5 - - - -
350C TYR* 3.7 24.1 - - - -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.0 20.5 + - - -
44A VAL 3.3 10.8 - - - +
45A LYS* 4.0 33.9 - - + +
58A GLY* 1.3 76.4 - - - +
60A PHE* 1.3 68.1 + - - +
61A GLU* 2.8 24.9 + - - -
79A LEU* 3.4 23.3 - - + +
80A ALA* 3.3 5.9 + - - -
81A TYR* 3.0 71.9 + - + +
98A TYR* 6.1 0.2 - - - -
17C VAL* 4.0 7.8 - - - +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 4.0 1.9 + - - -
42A LEU 5.6 1.1 - - - -
43A GLY* 3.2 4.0 - - - -
44A VAL* 2.8 51.1 + - + +
59A ARG* 1.3 75.5 - - - +
61A GLU* 1.3 68.5 + - - +
62A TRP* 3.9 24.5 - + + -
77A ASN* 3.6 32.5 - - + -
79A LEU 3.2 13.2 - - - -
80A ALA* 4.3 0.9 - - + -
17C VAL* 4.6 4.9 - - + +
40C VAL* 3.7 41.7 - - + -
42C LEU* 4.1 16.2 - - + -
62C TRP* 3.9 20.0 - + - -
64C THR* 4.0 13.7 - - + -
66C THR* 4.5 0.9 - - + -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 2.6 31.8 + - + +
41A ARG* 4.0 23.8 + - + -
42A LEU 3.6 8.5 - - - +
59A ARG* 2.8 17.7 + - - -
60A PHE* 1.3 78.7 - - - +
62A TRP* 1.3 57.9 + - - +
77A ASN* 3.7 2.4 - - - -
78A ARG* 2.6 70.0 + - + +
79A LEU* 2.8 36.5 + - + +
98A TYR* 5.1 0.5 + - - -
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Residues in contact with TRP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.9 1.8 - - + -
41A ARG* 3.2 7.8 - - - +
42A LEU* 2.8 66.3 + - + +
60A PHE* 3.9 21.0 - + + -
61A GLU* 1.3 74.7 - - - +
63A GLU* 1.3 64.9 + - - +
64A THR* 3.5 31.2 - - + -
75A ASN* 3.6 40.2 + - - +
76A LYS 3.3 19.5 - - - -
77A ASN* 3.6 18.3 + - - -
78A ARG* 4.6 0.9 - - - -
414A CA 4.6 12.6 - - - -
60B PHE* 4.0 25.1 - + - -
62B TRP* 4.4 17.5 - + - -
75B ASN* 5.6 0.2 - - - -
62C TRP* 4.4 13.3 - + - -
75C ASN* 4.9 0.8 + - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 4.6 0.7 - - - -
39A ARG* 4.1 34.1 + - + +
40A VAL 3.1 16.6 - - - +
41A ARG* 2.8 44.1 + - - +
62A TRP* 1.3 81.4 - - - +
64A THR* 1.3 62.2 + - - +
65A LYS* 5.5 4.3 - - + -
75A ASN* 3.6 0.5 - - - -
76A LYS* 2.7 57.0 + - + +
78A ARG* 3.7 23.4 + - - -
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 3.2 6.5 - - - +
40A VAL* 2.9 38.7 + - + +
62A TRP* 3.5 33.4 - - + -
63A GLU* 1.3 76.1 - - - +
65A LYS* 1.3 62.5 + - - +
66A THR* 3.8 5.7 + - + +
74A GLU 3.3 5.8 + - - -
75A ASN* 3.1 17.7 + - - -
60B PHE* 4.0 8.7 - - + -
77B ASN* 2.9 36.0 + - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASP* 2.9 29.2 + - - +
38A SER 3.7 21.4 + - - -
39A ARG* 3.5 27.7 - - + +
63A GLU* 5.5 4.3 - - + +
64A THR* 1.3 74.3 + - - +
66A THR* 1.3 60.7 + - - +
67A ASN* 3.5 17.9 + - - +
68A LYS* 5.3 1.3 + - + -
69A ALA 5.6 1.2 - - - +
72A GLU* 5.6 4.7 - - - +
74A GLU* 3.1 38.0 + - + +
76A LYS* 3.8 24.7 - - + +
77B ASN* 3.1 18.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il